Life Sciences Commons^™

Using Nmr Chemical Shift Perturbations To Map Interactions Between Acyl-Acyl Carrier Proteins And Acyl Homoserine Lactone Synthases, Madison N. Rizzo

Boise State University Theses and Dissertations

A pandemic of antibiotic resistance is underway and affecting multiple industries, including veterinary, agricultural, and healthcare. High bacterial population density is a major form of defense for bacterial cells against drugs, contributes to antibiotic resistance, and is one of the requirements for the formation of biofilms. Quorum sensing is a form of cell-to-cell communication that both gram-negative and gram-positive bacteria use to account for density behavior. When the population density of bacteria reaches a certain level (a “quorum”), there is an observed coordinated shift in gene expression that leads to optimized growth or virulence. Acyl carrier proteins (ACP) and the …

Dna Origami Scaffold Development For Digital Nucleic Acid Memory, Sarah Elizabeth Kobernat

Boise State University Theses and Dissertations

Recently, DNA nanotechnology has emerged as a promising and rapidly expanding method to utilize nucleic acids as a nanoscale building material. DNA origami is a major structural application of DNA nanotechnology, using DNA to construct two- and three-dimensional shapes. These structures have been employed for a variety of uses including DNA data storage. DNA is a promising material to address the impending shortage of silicon-based storage as data demands increase. There are many sequence-based methods of data storage, but digit Nucleic Acid Memory (dNAM) uses DNA origami as a breadboard and is read by super-resolution microscopy instead. dNAM uses DNA …

Structure, Function, And Immunogenic Applications Of Ab5-Type Adp-Ribosylating Bacterial Toxins, Elise Marie Overgaard

Boise State University Theses and Dissertations

Bacterial mono-ADP-ribosyltransferases (ARTs) catalyze the singular transfer of an ADP-ribose moiety from an NAD+ molecule onto a target molecule. ARTs contain an ancient and highly conserved tertiary structure and have a wide variety of intracellular targets and effects. Some, but not all, bacterial ARTs have an AB₅-type multimeric structure consisting of an enzymatically active subunit non-covalently situated atop of a non-toxic pentamer. The active, or A, subunit of AB₅-type toxins has a catalytic action that contributes to bacterial pathogenicity, and it is sometimes, but not always, an ART. ArtAB is an ART with AB₅-type …

Modulation Of Alpha-Crystallin-Membrane Association By Phospholipid Acyl Chain Length And Degree Of Unsaturation, Geraline Trossi-Torres

Boise State University Theses and Dissertations

Cataract is the leading cause of blindness worldwide. The only treatment for cataracts is the surgical removal of the cataractous lens and the replacement of an intraocular lens. With less availability of treatment and low income, the visual damage caused by cataracts can go untreated. The cataract may develop again after surgery, such as posterior capsule opacification. With age and cataracts, α-crystallin, a significant protein of the mammalian eye lens, is progressively associated with the eye lens membrane. The primary association sites of α-crystallin with the membranes are phospholipids. However, it is unclear if phospholipids’ acyl chain length and degree …

Improving The Ribozyme Toolbox: From Structure-Function Insights To Synthetic Biology Applications, Jessica Michelle Roberts

Boise State University Theses and Dissertations

Self-cleaving ribozymes are a naturally occurring class of catalytically active RNA molecules which cleave their own phosphate backbone. In nature, self-cleaving ribozymes are best known for their role in processing concatamers of viral genomes into monomers during viral replication in some RNA viruses, but to a lesser degree have also been implicated in mRNA regulation and processing in bacteria and eukaryotes. In addition to their biological relevance, these RNA enzymes have been harnessed as important biomolecular tools with a variety of applications in fields such as bioengineering. Self-cleaving ribozymes are relatively small and easy to generate in the lab using …

Biophysical Insights Into The Transport Properties Of Lysenin Channels, Andrew Merlin Bogard

Boise State University Theses and Dissertations

The defense work focused on deciphering novel functionalities of lysenin channels with respect to adjustment of their regulation and transport properties in response to environmental changes. Lysenin is a pore-forming toxin extracted from the earthworm E. fetida, which self-assembles into large pores in artificial and natural lipid membranes containing sphingomyelin. Prior investigations on their functionality identified strong regulation by voltage and ligands as fundamental traits of lysenin, similar to ion channels. In addition, stochastic sensing, controlled switching, and hysteretic conductance have been added to the list of intricate biophysical properties of lysenin channels as potential enablers of biotechnological and biomedical …

Modeling Developmental, Molecular, And Behavioral Effects Of An Apolipoprotein-E4 Fragment On The Embryogenesis Of Zebrafish, Madyson Mccarthy

Boise State University Theses and Dissertations

Although the increased risk of developing sporadic Alzheimer’s disease (AD) associated with the inheritance of the apolipoprotein E4 (APOE4) allele is well characterized, the molecular underpinnings of how ApoE4 imparts risk remains unknown. Enhanced proteolysis of the ApoE4 protein with a toxic-gain of function has been suggested and a 17 kDa amino-terminal ApoE4 fragment (nApoE4_1-151) has been identified in post-mortem human AD frontal cortex sections. Recently, we demonstrated in vitro, exogenous treatment of nApoE4_1-151 in BV2 microglial cells leads to uptake, trafficking to the nucleus and increased expression of genes associated with cell toxicity …

Mechanisms For Extracellular Matrix-Dependent Blood-Brain Barrier Dysfunction, Brian Adam Hoettels

Boise State University Theses and Dissertations

Dysfunction of the blood vessels that form the blood-brain barrier (BBB) is observed across various neurological disorders, including multiple sclerosis (MS). As barrier loss culminates in neuronal dysfunction and degeneration, a better understanding of the mechanisms underlying BBB dysfunction is needed.

Tight junctions are multiprotein complexes maintained by the endothelial cells lining the inner blood vessel wall to seal the intercellular space, and their disruption impairs BBB function. In my first chapter, I focus on how tight junctions are altered in CNS inflammatory demyelinating diseases (CNS-IDDs) like MS as BBB dysfunction is one of the earliest known stages in …

Liposomes: Production And Applications For Controlled Drug Delivery, Gamid Abatchev

Boise State University Theses and Dissertations

This dissertation recognizes the enormous potential presented by the ever-evolving development of liposomes as drug carriers and seeks to offer further investigation into their useful production and utilization. The first chapter presents the basic principles governing their formation by self-assembly in water solutions, briefly describes the most common production methods, and points out essential past advances that led to their use as drug carriers. Chapter two exemplifies production of liposomes by the traditional methods of extrusion and sonication, detailing passive and active loading, as well as physical characterization by Dynamic Light Scattering, microscopy imaging, and fluorescence spectroscopy. In the next …

Role Of The Nuclear Envelope In The Mechanoregulation Adipogenesis, Matthew H. Goelzer

Boise State University Theses and Dissertations

Mechanical signals are known regulators of mesenchymal stem cell (MSC) fate, regulating their differentiation into osteoblasts, chondrocytes, and adipocytes. These relevant mechanical signals reach to nucleus through nuclear envelope proteins such as Lamin A/C and the Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes. Within the context of bone, clinically relevant mutations of Lamin A/C and the LINC complexes have been shown to alter adipogenic and osteogenic MSC differentiation patterns, suggesting that that nucleo-cytoskeletal connectivity provided by nuclear envelope is important in regulating MSC fate. Using MSC adipogenesis as a model of MSC mechanical regulation, the goal of this work …

Engineering Of Recombinant Fortilin For Structure Activity Studies, Maranda S. Cantrell

Boise State University Theses and Dissertations

Cardiovascular disease (CVD) is the leading cause of death worldwide affecting approximately 40% of all adults over the age of 20 and is responsible for an economic burden upwards of $3 billion annually. Treatments for CVD are limited to either hypertension medication to treat symptoms, and/or statin-based drugs to reduce low-density lipoprotein (LDL) cholesterol formation. However, recent studies suggest that approximately 50% of patients diagnosed with CVD have normal to low LDL cholesterol levels. Therefore, a critical need exists to develop new treatments for CVD that are independent of cholesterol lowering statins. Fortilin, also known as translationally controlled tumor protein …

The 4d Living Genome, Julianna Arlene Sherman Goelzer

Boise State University Theses and Dissertations

Over the last few decades great advances have been made in our understanding of gene expression and the human genome. In 2003 the human genome was sequenced for the first time, allowing us to discover its true importance in human health. While sequencing the human genome was a great advance, it ultimately created more questions than it answered. It is known that the genomic sequence is extremely important in genome regulation, however recent studies have shown that the 4D (spatiotemporal) organization and dynamics of the living genome plays an equally critical role in regulation of gene expression. A key factor …

Collagen Xi Impact On Structure And Function Of The Vertebrate Inner Ear In A Zebrafish Model, Makenna Hardy

Boise State University Theses and Dissertations

The ear is essential to maintaining balance and hearing; both of which can be linked to one another and significantly impact a person’s quality of life. Although aging and damage are more common reasons for hearing loss, congenital ear defects still have a considerable impact on our population. The function of the ear can be affected by structural deformities to the ear and its components which results in hearing loss. Mutations and single nucleotide polymorphisms in the gene encoding Collagen XI alpha one chain (COL11A1) protein can play a role in hearing and balance dysfunction in humans as seen in …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Regulation Of In Vitro And In Vivo Hepatic Stellate Cell Activation By The Ayrl Hydrocarbon Receptor, Shivakumar Rayavara Veerabhadraiah

Boise State University Theses and Dissertations

Liver fibrosis is a pathological condition characterized by the excessive deposition of extracellular matrix material by activated hepatic stellate cells (HSCs). We recently reported that activation of the aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) increases HSC activation in vitro and in mouse models of experimental liver fibrosis. The goal of this project was to determine the mechanism by which AhR activation impacts HSC activation and the subsequent development of liver fibrosis. It is possible that HSCs are direct cellular targets for TCDD. Alternatively, TCDD could increase HSC activation indirectly by exacerbating hepatocyte damage …

Identification And Characterization Of Candidate Staphylococcus Aureus Antigens For Inclusion In A Multivalent Bovine Mastitis Vaccine, Danielle Scarbrough

Boise State University Theses and Dissertations

Bovine mastitis, inflammation typically caused by bacterial infection, is the most prevalent disease affecting the global dairy industry. Staphylococcus aureus remains one of the most important pathogens implicated in the disease and can persist within herds at subclinical levels. A preventative S. aureus bovine mastitis vaccine would substantially lessen costs associated with treatment and restore revenue lost due to decreased milk production. One such experimental vaccine is the IsdA-CTA₂/B + ClfA-CTA₂/B vaccine, containing the S. aureus antigens IsdA and ClfA , each fused to the nontoxic A₂/B subunits of cholera toxin, which serves as …

Analytic Solutions For Diffusion On Path Graphs And Its Application To The Modeling Of The Evolution Of Electrically Indiscernible Conformational States Of Lysenin, K. Summer Ware

Boise State University Theses and Dissertations

Memory is traditionally thought of as a biological function of the brain. In recent years, however, researchers have found that some stimuli-responsive molecules exhibit memory-like behavior manifested as history-dependent hysteresis in response to external excitations. One example is lysenin, a pore-forming toxin found naturally in the coelomic fluid of the common earthworm Eisenia fetida. When reconstituted into a bilayer lipid membrane, this unassuming toxin undergoes conformational changes in response to applied voltages. However, lysenin is able to "remember" past history by adjusting its conformational state based not only on the amplitude of the stimulus but also on its previous …

Dimerization Of The Notch Intracellular Domain Results In Distinct Signaling Activity, Jacob Jeffery Crow

Boise State University Theses and Dissertations

The Notch signaling pathway is a core component of multicellularity; enabling cells to directly communicate with both their neighbors and the surrounding microenvironment. These signals are translated directly through the Notch proteins, where a fragment of Notch transitions into the nucleus to act as a co-transcription factor, setting into motion a host of physiological responses. Commonly involved in pathways that define a cell’s identity and fate decisions, what appears to be a simplistic pathway instead exists in a state of high-tunability and strict control. Missteps in this pathway are generally embryonically lethal or lead to a suite of congenital disorders …

Analyzing Change-Of-Direction And The Laterally Resisted Split Squat: Incorporating A Lateral Vector Into The Single Leg Squat, Derek Maddy

Boise State University Theses and Dissertations

Improving change of direction (COD) with the use of strength training has led to mixed results. To date, the modified single leg squat (MSLS) and the bilateral squat (BS) have been successfully used to improve COD, with equal improvement. COD is primarily performed at a 45-75° frontal plane angle; however, the MSLS and BS are performed at a 90° frontal plane angle. Based on the force vector theory, it is proposed that a more mechanically similar strength training exercise, the Laterally Resisted Split Squat (LRSS), be used. The purpose of this study is to compare COD with the LRSS, MSLS, …

Genetic Analysis Of Invasive Populations Of Ventenata Dubia (Poaceae): An Assessment Of Propagule Pressure And Pattern Of Range Expansion In The Western United States, Inna Pervukhina-Smith

Boise State University Theses and Dissertations

Molecular markers prove to be an invaluable tool in assessing the introduction dynamics, pattern of range expansion, and population genetics of an invasive species. Ventenata dubia (Leers) Coss. (Aveneae; ventenata) is a diploid, primarily self-pollinating, annual grass native to Eurasia and Northern Africa. The grass has a detailed herbarium collection history in the western United States since its discovery in eastern Washington in 1952. Genetic analysis of 51 invasive populations (1636 individuals) of V. dubia, coupled with historical records, suggests moderate propagule pressure from multiple introductions, followed by local or regional range expansion. Enzyme electrophoresis detected nine multilocus genotypes …

Structure And Bioactivity Of A Rationally Designed Nicotinic Acetylcholine Receptor Antagonist Targeting The Alpha-3 Beta-2 Subtype, Leanna Marquart

Boise State University Theses and Dissertations

The work presented in this thesis contributes to ongoing development of an efficient workflow for identification of lead compounds, based on the molecular scaffold of α-conotoxin MII, for drug therapies targeting nicotinic acetylcholine receptors. Nicotinic acetylcholine receptors (nAChRs) are pentameric, ligand-gated ion channels with distribution throughout the central nervous system and are implicated in a variety of neurological diseases including schizophrenia, nicotine addiction, Alzheimer’s disease, and Parkinson’s disease. However, ligand effect on nAChR function is not well understood. Consequently, drug therapies for neurological diseases either do not exist, or have short-lasting efficacy and/or severe side effects. Barriers to the comprehension …

Investigating Autophagy Dysfunction Induced By A Parkinson's Disease-Causing Mutation In Vps35, Abir Ashfakur Rahman

Boise State University Theses and Dissertations

Parkinson’s Disease (PD) is an idiopathic disorder with no known cure. With number of cases steadily rising around the world, it is imperative to turn to the underlying cellular and molecular mechanisms of the disease manifestation and neurodegeneration to craft novel modes of therapy. VPS35 is one of the few genes that have identified and definitively linked to familial PD. The particular mutation that has been associated is known to cause dysfunction of a key cellular process known as autophagy. This process is primarily responsible for clearance of unwanted, damaged or misfolded proteins, among other things. Our study reveals an …

Harnessing The Physical Properties Of Zno Nanoparticles For Biological Applications And Factors That Impact Zno Nanoparticle Toxicity, Joshua Eixenberger

Boise State University Theses and Dissertations

The production of materials at the nanoscale leads to novel properties and has made the field of nanotechnology a part of everyday life. Numerous applications of nanomaterials have led to their use in electronics, optics, and medicine. However, creating materials at such a small size brings them on the same scale as many biomolecules and cellular components, altering their interactions with biological systems. This can lead to unintended biological impacts as many nanomaterials are considerably more toxic than their bulk counterpart material. ZnO nanoparticles (nZnO) are particularly interesting in this context. The FDA classifies ZnO as a generally recognized as …

Developing Ultra-High Throughput Sequencing Based Assay For Ligase Ribozymes For The Study Of Evolutionary Innovations, James Collet

Boise State University Theses and Dissertations

The study of evolutionary innovations, or novel traits, is integral to understanding evolution yet is poorly understood. By studying the regions between genotype networks that produce the same phenotype, we can better characterize the process by which innovation occurs. The overarching goal of this study is to assign fitness values to the overlapping genotype network of two catalytic RNA molecules, or ribozymes. Properly characterizing this region requires the study of thousands of individual sequences, which is achievable through the use of high-throughput sequencing analysis. This thesis focuses on developing assays for one of the ribozymes, the ligase ribozyme. Due to …

The Regulation Of Notch Signaling By Src Kinase And Polyphenolic Compounds, Bryce David Lafoya

Boise State University Theses and Dissertations

Cellular signaling pathways provide cells with the means to sense their environment and communicate with other cells. The Notch signaling pathway is comprised of a set of protein machines which work in unison to coordinate cellular processes in response to stimuli coming from neighboring cells and changing microenvironmental conditions. Notch signaling is an important mode of cellular communication which is crucial to many processes involved in development and disease. During Notch activation, information about the extracellular environment is fed into the cell and relayed to the nucleus through a number of biochemical processes. The information-rich messages carried by Notch signaling …

Investigation Of Catalytic Activity Of Stable Β-Ketoacyl-Acp Substrate Analogs In Quorum Sensing Signal Synthesis, Nhu Lam

Boise State University Theses and Dissertations

Quorum sensing is an intercellular mechanism used by many bacterial pathogens to regulate behaviors, such as motility, virulence, and antibiotic production. Disruption of quorum sensing is shown to be deleterious to bacterial pathogenicity, without causing lethality. In Gram-negative bacteria, acyl-homoserine lactone (AHL or acyl-HSL) signal molecules are synthesized by AHL synthase enzymes using acylated-acyl carrier protein (acyl-ACP) and S-adenosyl-L-methionine (SAM) as their substrates. Pantoea stewartii EsaI, which causes Stewart’s wilt in corn, and Yersinia pestis YspI, which causes bubonic plague are AHL synthases that use 3-oxohexanoyl-ACP and 3-oxooctanoyl-ACP as the acyl-substrate to synthesize 3-oxohexanoyl-HSL and 3-oxooctanoyl-HSL signals, respectively. Unfortunately, the …

Acyl-Homoserine Lactone Based Modulators For Rhli, A Quorum Sensing Signal Synthase In Pseudomonas Aeruginosa, Daniel D. Shin

Boise State University Theses and Dissertations

Gram-negative bacteria use N-acyl-homoserine lactone (AHL) autoinducer based signal system, known as quorum sensing (QS), to modulate the gene expression for such traits as biofilm formation, toxin production, and antibiotic resistance. Therefore, there is great potential in pursuing quorum sensing inhibition (QSI) as a means of achieving antivirulence. Pseudomonas aeruginosa, an opportunistic pathogen commonly found in healthcare-related infections, use two LuxI/R type systems to regulate AHL-based quorum sensing: LasI/R and RhlI/R. LasI (initiator protein/signal synthase) and LasR (receptor) use 3-oxododecanoyl-L-homoserine lactone signal molecule while RhlI and RhlR use butanoyl-L-homoserine lactone autoinducer. Thus far, most of the studies have …

Examination Of Klebsiella Pneumoniae 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase And 5-Methylthioribose Kinase, Jason Alan Stonick

Boise State University Theses and Dissertations

Klebsiella pneumoniae is an opportunistic bacterial pathogen that is emerging as a major global threat as an infectious agent. This organism, along with many other pathogens, possesses a broad suite of antibiotic resistances that can make treatment exceedingly difficult. As such, the impetus for creating novel antibiotics is at an all-time high despite the fact that pharmaceutical investment into drug development is at an all-time low. S-adenosylmethionine (SAM) is a universally utilized metabolite involved in a wide array of biosynthetic processes, and whose products are catabolized by a different set of enzymes in mammals than used by many bacteria, protozoa, …

Analysis Of Novel Mta Nucleosidase Inhibitors As Anti-Parasitic Agents, Teslin Marie Botoy

Boise State University Theses and Dissertations

The parasitic protozoa Giardia intestinalis and Entamoeba histolytica are major health concerns and responsible for hundreds of millions of cases of intestinal disease per year. Strains of both parasites have been discovered that show resistance to metronidazole, the most prevalent treatment for these pathogens. Thus, there is a need to identify new drugs and drug targets to combat the growing threat of drug resistant parasites. The parasite enzyme methylthioadenosine nucleosidase (MTN) is one such potential target. Traditional drug development processes take almost a decade and hundreds of millions of dollars to complete. In an effort to shorten that timeline and …

Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia

Boise State University Theses and Dissertations

VPEvolve is a free and open source application that utilizes a Visual Programming Environment (VPE) for the setup of the Genetic Algorithm (GA), for optimization of computational models. Specifically, the User Interface uses connected glyphs to represent the genetic operators of mutation, reproduction, fitness and selection. These glyphs give the user an intuitive way to set the parameters for the GA, and better visualization of the population's flow through these operators.

VPEvolve is currently being developed alongside research being done in Biocomputing to create models of cellular regeneration based on the regenerative properties of Planaria or flatworms. Since these models …